diff --git a/docs/release-notes/v1.50-v1.59.md b/docs/release-notes/v1.50-v1.59.md index a9894033..b15692c3 100644 --- a/docs/release-notes/v1.50-v1.59.md +++ b/docs/release-notes/v1.50-v1.59.md @@ -528,7 +528,7 @@ Please review the documentation, as these changes may impact your integrations. * ??? abstract "Introduced changes to Tabular Data" - + | Introduced change | Changes Description | |:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| @@ -540,7 +540,7 @@ Please review the documentation, as these changes may impact your integrations. * ??? danger "Affected endpoints (for both as-curator and as-users)" - + | Endpoint Group | Endpoints Affected | |:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------| @@ -553,7 +553,7 @@ Please review the documentation, as these changes may impact your integrations. * ??? abstract "Introduced changes to Variants" - + | Introduced change | Changes Description | |:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| @@ -564,7 +564,7 @@ Please review the documentation, as these changes may impact your integrations. * ??? danger "Affected endpoints (for both as-curator and as-users)" - + | Endpoint Group | Endpoints Affected | |:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------| @@ -586,7 +586,7 @@ Please review the documentation, as these changes may impact your integrations. ![RN](1.58/1-58-4.png) * ??? danger "Affected endpoints (for both as-curator and as-users)" - + | Endpoint Group | Endpoints Affected | |:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------| diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/10DataClass.png b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/10DataClass.png new file mode 100644 index 00000000..d8fd712c Binary files /dev/null and b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/10DataClass.png differ diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/11Bookmarks.png b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/11Bookmarks.png new file mode 100644 index 00000000..0b44e9a0 Binary files /dev/null and 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a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/three_dots_menu.png and /dev/null differ diff --git a/docs/user-guide/doc-odm-user-guide/studybrowser.md b/docs/user-guide/doc-odm-user-guide/studybrowser.md index 5a8c144e..9c3b9f12 100644 --- a/docs/user-guide/doc-odm-user-guide/studybrowser.md +++ b/docs/user-guide/doc-odm-user-guide/studybrowser.md @@ -1,84 +1,118 @@ # Study Browser -The Study Browser is the main interface to quickly search and discover studies of interest. +The Study Browser is the main interface to quickly search and discover studies of interest. + +!!! Important + Without **Access all data** permission you can access only studies created by you or shared with a group you belong to. You can access all studies in the ODM with **Access all data** permission. Refer to the section [User Setup](setup.md) to learn more about users and permissions. ## Getting to the Study Browser -Click ‘Browse studies’ on the dashboard after you sign in to launch the Study Browser. +You can access the list of available studies by clicking on **Browse Studies** from the dashboard, or by clicking at the top left menu and selecting **Study Browser**. + +![1StudyBrowser.png](doc-odm-user-guide/images/1StudyBrowser.png) +
Access the available studies in ODM (based on your permissions) by clicking Browse studies on the main dashboard (A), or by clicking on the top left menu and selecting Study Browser (B).
+ +* Under the study title there is a summary of the metadata that is associated with the study. +This displays information such as the organism, tissue, cell-type, disease and so on and is pulled straight from the metadata fields of the samples in the study. +* You can hover over any name in the summary column and the name of the metadata field where the data comes from will appear. +* There is also information of who imported the study into ODM and when. +* To the right of the study title you can see how many samples are present in the study and which Data Classes are associated with it. + + +## Search for Data + +At the top of the window is the main search bar. You can search by the name of a study, the accession number, sample or signal object, or any text within any metadata field across all data visible to you. + +* As you type, autocomplete suggestions based on dictionaries of terms present in ODM will appear. + +![2SearchForData.png](doc-odm-user-guide/images/2SearchForData.png) +
Search for data. The system provides an autocomplete feature that offers values for different ontologies in the search bar. For example, if you type bowe, the system will suggest autocompleting options containing the word bowe
+ +* The search is synonym-aware, meaning if you type in **‘human’**, it will suggest *Homo sapiens* and include results for synonyms. -![image](doc-odm-user-guide/images/quickstart_user_dashboard.png) +![3SearchForData.png](doc-odm-user-guide/images/3SearchForData.png) +
Search for data. The system will suggest autocomplete options based on preferred ontologies. For example, if you type human, the system will suggest the label "Homo sapiens"
-You can also use the short cut dock in the top lefthand corner of any window. +* Use question marks (?) to match any character. -![image](doc-odm-user-guide/images/shortcut_1_37.png) +![4SearchForData.png](doc-odm-user-guide/images/4SearchForData.png) +
Search for data. Use question marks to match any missing characters. For example, if you type the word c?ncer, the system will suggest studies containing the word cancer
-## Exploring the Study Browser +* Use asterisks (\*) to allow any number of wildcard characters. -![image](doc-odm-user-guide/images/quickstart_user_studybrowser.png) +![5SearchForData.png](doc-odm-user-guide/images/5SearchForData.png) +
Search for data. Use asterisks to allow any number of wildcard characters. For example, if you type *ale, the system will display studies containing the words male and female
-At the top of the window is the main search bar. In the text box you can search by the name of a study, -the accession of a study, sample or signal object, or by any text that is in any metadata field across -all of the data you have visibility of. As you begin typing you will be offered auto-complete suggestions -based on dictionaries of terms that are present in ODM. +* Use quotes (“ ”) to search for an exact phrase. -The search is synonym-aware (exact and related), so if you type in ‘human’ the auto-complete suggests ‘Homo sapiens’ as the preferred label of humans and the results from synonyms are automatically included in search results. +![6SearchForData.png](doc-odm-user-guide/images/6SearchForData.png) +
Search for data. Use quotes to search for an exact phrase or word. For example, if you type “single cell”, the system will display studies that contain the words single cell in metadata
-Question marks (?) match any character, and you can use asterisks (\*) to allow any number of (including zero) wildcard characters: +* Terms can be joined with the **AND** operator (by default the OR operator is used), and they can be excluded with a preceding **NOT**. -``` -* -``` +![7SearchForData.png](doc-odm-user-guide/images/7SearchForData.png) +
Search for data. The use of operators will display a different number of available studies depending on the specific functions: OR will display studies where one or the other conditions are met; NOT will display studies where one condition is met but not the other; whereas AND will display studies where two conditions are met
-ale will find “male” and “female” for example. Use quotes (“”) to search for an exact phrase. For example, “single cell” will find results that contain the whole phrase only. +* The main panel displays your search results and filter options. If no search is performed, all studies accessible to your user account are displayed, ordered by date with the newest at the top. -Terms can be joined with the AND operator (by default the OR operator is used), and they can be excluded with a preceding NOT. +![8Studies.png](doc-odm-user-guide/images/8Studies.png) +
Search for data. If no filters are applied, the system displays the list of all the available studies within the ODM
-The main panel displays the results of your search and filter options, if you have any, -otherwise all studies are displayed that your user account has visibility of, -ordered by date with the newest at the top. +* If your search term matches a term from an ontology with child terms, you can toggle **extend query** to include child terms in the search results. +* This feature is available if the total number of terms (including synonyms) is fewer than 30,000. -If your search term matches a term from an ontology which has child terms, then once initial results have been retrieved there is the option to toggle ‘extend query’, which will add search results for child terms (those with the subClassOf property in the ontology). This is only available if the number of terms (including synonyms) is fewer than 30,000. +![9SearchForData.png](doc-odm-user-guide/images/9SearchForData.png) +
Search for data. Extend the query to include child terms in the search results. For example, the number of available studies with the word cancer increases when the option Extend query is selected
-### Filter panel +## Filter Data -The filter panel allows you to filter your results with search facets. Set facets to refine search results. Facets are -automatically generated from the metadata of available datasets, and the suggested list of facets varies -depending on a search results. Click ‘More’ to explore the whole list of suggested items. +* By default, all studies you have permission to access are displayed. Given the potential number of studies, search and filtering options in the left-hand panel of the **Study Browser** help you find specific studies of interest. +* You can search by study name, accession number, or any relevant metadata field. +* The facets beneath the search bar allow you to filter search results based on sample metadata fields. -![image](doc-odm-user-guide/images/studybrowser_searchpanel.png) +![10DataClass.png](doc-odm-user-guide/images/10DataClass.png) +
Filter data. Use the filters to narrow the search of studies. For example, select Data Class and then tick the option Single-cell transcriptomics to find exclusively studies containing single-cell data
-Bookmarked studies can be shown by clicking on the Bookmarks icon. Access allows you to see your studies, those that are accessible to you (for example, public studies) or those that have been shared with your user account/group. +## Bookmark studies -If there are additional facet terms a **Find more** link will be displayed. -Clicking on this allows you to type in terms and you can select from the presented list of options. +* You can save preferred studies for easy access. To the left of a study title is a three-dot link. Click this to open a menu that allows you to share the study (if you are the owner) and save it to bookmarks. -![image](doc-odm-user-guide/images/studybrowser_autocomplete.png) +![11Bookmarks.png](doc-odm-user-guide/images/11Bookmarks.png) +
Bookmark studies. Save preferred studies to access them easily. To do so, click on the three-dot link next to the name of the study and click on Save to bookmarks
-### Configuring the filter panel +* Bookmarked studies are accessible by clicking on the Bookmarks icon. This section displays your studies and those shared within the groups you belong to, providing access to all studies available to you. Note that studies are not shared with individual users but are instead shared within groups. -Exactly which metadata fields are available as search facets can be configured by users who have the permission to configure facets. To change the facets click the cog icon at the bottom of the filter panel. +![12Bookmarked2.png](doc-odm-user-guide/images/12Bookmarked2.png) +
Bookmarked studies. Bookmarked studies are accessible by clicking on the button Saved. A new window will appear where you can access the saved studies or remove the bookmark if needed
-![image](doc-odm-user-guide/images/configure-facets.png)![image](doc-odm-user-guide/images/configure-facets-screen.png) +## Configuring the filter panel -You can add facets to the filter panel by clicking the **New facet** button and typing the full name of the metadata field which you want to appear. Names are case sensitive. You can also reorder the facets by dragging the icon next to the facet name, or delete them from the panel by clicking the bin icon. Once you are happy click the **Save** button to apply the changes. If your facet is empty or a duplicate it will not be allowed and the panel change won’t save until this is corrected. +!!! Important + You can only access the Configure facets option if you have the **Configure facets** permissions. For access, an admin must edit the settings. Refer to the [User Setup](setup.md) section for more information. -### Results panel +Users with permission **Configure facets** can customize which metadata fields are available as search facets. -![image](doc-odm-user-guide/images/quickstart_user_studybrowser.png) +To do this: -The main panel in the study browser shows the results of your search, or if no search terms/filters have been applied, all studies that you have visibility of. The first column displays the name of the study, and you can click this to look at the study in more detail. It also lists information about which user created or imported the study, and the date. +1. Click the cog icon at the bottom of the filter panel to change the facets. +2. Add facets by clicking the **New Facet** button. +3. Type the exact name of the metadata field (names are case-sensitive). -To the left of the study titles is a three dot link. Click this to open a menu that allows you to share the study (if you have permission), export data, copy the accession of the study, add it to your bookmarks, or view more information. +You can reorder facets by dragging the icon next to the facet name or delete them by clicking the bin icon. Click the **Save** button to apply changes. The panel will not save if your facet is empty or a duplicate. -![image](doc-odm-user-guide/images/three_dots_menu.png) +![13Facets.png](doc-odm-user-guide/images/13Facets.png) +
Configure facets. Reorder the facets to display for searching studies. Click on Configure facets at the bottom left of the page. A new window will open where you can add, rename, delete or drag facets. The changes will apply after clicking on Save
-Under the study title there is a summary of the metadata that is associated with the study. This displays information such as the organism, tissue, cell-type, disease and so on and is pulled straight from the metadata fields of the samples in the study. +## Navigation and Help -You can hover over any name in the summary column and the name of the metadata field where the data comes from will appear. +* Use the shortcut dock in the top left-hand corner of any window to return to the main dashboard. +* Click on Quick Guide in the top right of your window for reference guides and examples on how to use ODM. -![image](doc-odm-user-guide/images/studybrowser_tooltip.png) +![14NavigationUpdated.png](doc-odm-user-guide/images/14NavigationUpdated.png) +
Navigation and help. Click on the left panel to return to the main dashboard. Click on the button to explore Quick Guide
-There is also information of who imported the study into ODM and when. -To the right of the study title you can see how many samples are present in the study. +* On the right side of the board, you can access account details and check the status of any tasks you are running. +* Click the question mark next to the search bar to open the search help section for more details about advanced search functionality. -And finally you can use the bookmark flag at the end to flag studies for viewing later. +![15Help.png](doc-odm-user-guide/images/15Help.png) +
Navigation and help. Click on the question mark symbol (?) to open the search bar help section including operators, ontologies, and wildcards. Click on the Tasks option to visualize the status of any task you are running. Click on View all to visualize the last tasks you have run and their status (running, done, failed, etc.).